Access Technology Program Seminars

Spatial discoveries happen at many scales – at spatial whole transcriptome to spatial single cell. And, regardless of whether you’re looking to discover new biomarkers, or understand how disease progresses, or building a cell atlas of your tissue, the solutions and team at NanoString are the ones that will get you to your discoveries faster.

WideSeq, a service offered by the Purdue Genomics Core, spans the gap between small Sanger and large Illumina sequencing tasks. This allows, for example, sequencing of an entire plasmid construct at an affordable cost. Any double-stranded DNA template up to around 100 kb can generate useful results. Various use cases will be discussed. Sanger sequencing costs orders of magnitude more per base of sequence generated than Illumina Next Generation sequencing. But the costs of Illumina sequencing are in units of “runs”, rather than individual reads or bases. Even the smallest Illumina run generates vastly more sequence than is useful or cost-effective to deploy against a Sanger-level task. The Purdue Genomics Core gathers samples submitted to it, constructs Illumina libraries from them to be run on a MiSeq once per two weeks. Some informatics, like de novo assembly, are performed and the results returned as a web page

What is the one thing in life that completely affects us on multiple levels? It can affect us not only physiologically, but also mentally. This one thing also has the ability to be beneficial and detrimental. The answer is stress. By decreasing stress in our animal subjects during sampling we can produce higher quality data sets with fewer animals. The Purdue Translational Pharmacology (PTP) facility uses the Culex Automated Sampling System for rodents and swine to minimize pain and distress often caused by traditional sampling methods, which in turn produces quality data for our researchers. On top of reducing stress, the Culex automated sampling system can be used to collect multiple data sets from the same animal allowing you to reduce inter-animal variability in your studies. Please join us in finding out more about what the PTP can offer.

The IU School of Medicine Center for Proteome Analysis (CPA) utilizes state-of-the-art mass spectrometry techniques to quantify and detect changes in protein abundance, post-translation modifications, and stability. Recent projects have included sample types ranging from mouse brain regions, skeletal muscle, serum, subcellular fractionations, and even crickets! This presentation covers some current applications within the CPA.

The Chemical Genomics Core Facility is equipped with various high-throughput technologies to aid PIs in traditional chemical compound screening, plate-based assay development, new arrayed CRISPR screening, and high content analysis using high-throughput microscopic imaging. We serve as a bridge between your concept studies to future drug discovery.

Since the early 1980’s, the Indiana University Center for Survey Research (CSR) has partnered with world-class researchers to plan for, gather, and analyze high-quality data that advance knowledge and humankind. The CSR has conducted thousands of quantitative and qualitative research projects, using surveys, interviews, focus groups, and a wide range of other methods, including collection of medical specimens and environmental samples. In this presentation, we will take you on a journey through our diverse set of services from questionnaire design and survey programming to medical specimen collection and coding of qualitative data. We will also spotlight past collaborations that have used survey science with high real-world impact in improving health and well-being.

The purpose of this presentation is to describe the generation of conditional alleles in mice using the DEgradation based on Cre-regulated Artificial Intron (DECAI) approach. CRISPR-mediated insertion of the short DECAI cassette within exon 3 of Scyl1 and the functionality of the allele are reported. This strategy has the potential to simplify the process of generating mice with conditional alleles

The Preclinical Modeling and Therapeutics Core (PMTC) is a recently consolidated core consisting of the Angio BioCore and the In Vivo Therapeutics Core. The PMTC facilitates the development and testing of pharmacological and cellular therapies for cancer. It provides advanced resources essential for the preclinical validation of novel drug targets and biomarkers of cancer. In this seminar, the team will provide a brief overview of services offered. This will be followed by focused discussions on the Incucyte S3 Live-Cell Analysis (Sartorius) for in vitro cellular response studies and the IVIS SpectrumCT In Vivo Imaging System (PerkinElmer) for in vivo tracking of tumor response.

Proteins are the building blocks of life. During this seminar we will take a closer look at how we can use these molecules for multiple biotechnological applications including diagnostics, therapy, chemical synthesis, etc. The proteins, however, mostly need to be engineered at both protein or gene level to meet the conditions required for industrial applications or for production.For example, some enzymes require that are active at extreme conditions, such as high temperature or very low pH. Low cost is in general a main concern for multiple applications therefore engineering cells and proteins for high production is very important. This seminar will describedifferent problems that we encounter when taking proteins from nature and trying to use them for an industrial application and it will discuss the methods that we are using for making them fit for the biotechnological process.

Mass spectrometry (MS)-based proteomics is routinely applied to address a large range of biological questions, mainly because of its unparalleled ability to acquire high-content quantitative information about biological samples of enormous complexity. The core MS technologies, including the instrumentation and the methods for data acquisition and analysis, have significantly advanced, and will continue to advance in the quest for further improvement in sensitivity, throughput and proteome coverage. In this presentation, I will highlight various proteomics approaches that are currently applied at the Purdue Proteomics Facility, and their impact on understanding cell biology and diseases. Citing specific examples, I will discuss how functional proteomics has been used to learn about the molecular mechanisms of complex biological processes; how to design a successful proteomic experiment tailored to a specific project or biological question; and what additional methods can be integrated to make important biological discoveries. Finally, I will discuss how these lessons or new discoveries might guide future applications.

The Behavioral Phenotyping Core (BPC) is located within the Stark Neurosciences Research Institute at the Indiana University School of Medicine. The BPC has diverse capabilities to evaluate in vivo physiology and behavior of mice and rats. During this seminar you will learn about the automated technology we use to characterize sensory, motor, and autonomic functioning. We have multiple techniques to phenotype affective, motivational, and cognitive domains of behavior that may be altered by genetic, environmental, and pharmacological manipulations. Finally, we will discuss the power of linking behavioral outcomes with your pathology or ‘omics endpoints.

Nuclear Magnetic Resonance (NMR) spectroscopy enables analysis of natural products, metabolites, synthetic drug candidates, peptides, and proteins to determine their purity, structures, and interactions. Compounds in complex mixtures may be identified based on diffusion coefficients as well as by directly fitting the component spectra. Binding interactions are sensitively detected and mapped on the molecular structures while binding kinetics are accessible from NMR line shapes in titration experiments. This seminar will highlight the most NMR prominent capabilities relevant to biomedical research and drug design available to CTSI researchers at the Magnetic Resonance Research Center at the University of Notre Dame.

The Biospecimen Collection and Banking Core has been created to house four separate biospecimen collection entities which were part of the IU Simon Comprehensive Cancer Center. This talk will share which facilities are included and what services the Core will offer. Bring any questions you might have on the collection, processing and use of biospecimens in your research.

Single-cell RNA (scRNA) analysis technologies have emerged as powerful tools for in-depth analysis of cellular heterogeneity of different cell types and rare populations. Cell sorting is an indispensable tool used within the single-cell transcriptomics workflow. It delivers highly pure and viable target cells and nuclei for sequencing reactions resulting in an overall improvement of the results. In this talk, we will discuss how the Sony Cell Sorters have been used in this workflow and why the use of microfluidics chip provides a plug-and-play solution to users, enabling a streamlined approach in this application. Best practices used for sorting different cells, tissues and nuclei will also be discussed.

Dive deeper into disease pathology with 10x Genomics Visium Spatial Products, which allow you to understand your tissue sample like never before by profiling spatial gene expression alongside histological analysis of H&E stained sections to examine tissue anatomy or immunofluorescence for protein detection. Map the whole transcriptome with morphological context or focus on your genes of interest using targeted gene expression panels—choose from pre-designed panels or design your own—to make novel discoveries in normal development, disease pathology, and clinical translational research.

During this seminar you will learn about the benefits of MicroScale Thermophoresis (MST), an immobilization-free tool for quantitative analysis of molecular interactions using minimal sample volume. MST measures a broad range of binding affinities for many types of interactions by detecting changes in fluorescence intensity while a temperature gradient is applied over time. Different interaction measurements will be discussed that are possible with the Monolith NT instruments currently available at the Chemical Genomics Facility at Purdue Institute for Drug Discovery. Bring your questions for deciding on the best conditions to measure your interactions of interest.

The CODEX system facilitates multiplexed imaging of 50+ probes within thin-sectioned tissue by utilizing a panel of antibodies conjugated to unique DNA barcodes. The tissue sample is incubated with the full panel of antibody-DNA conjugates, which are then labeled with fluorescent probes and imaged three at a time. The fluorescent probes are then stripped, and another set of three fluorescent probes are added, imaged and stripped. The process is repeated for multiple cycles, giving you a highly multiplexed image of entire millimeter-scale samples. A member of the Indiana Center for Biological Microscopy, Dr. Connor Gulbronson will be discussing the technique, describing improvements that he’s made to the CODEX system and demonstrating the new HALO image analysis software available in the core facility.

In this seminar we will present a method for the exploratory analysis of lipids named multiple reaction monitoring (MRM)-profiling. The method employs a different analytical strategy compared to untargeted lipidomics by LC-MS. First, there is no liquid chromatography; the lipid extracts are injected directly into the source of the mass spectrometer, which confers speed to the analyses. We then trust the mass spectrometer to do the separation of the ions “internally” by using scan types that can profile chemical functionalities, and specific combinations of parent (intact) and fragment ions related to specific lipid classes. The parent-fragment ion scan is known as the MRM scan, and it is the most sensitive scan type in mass spectrometry. The MRM scan data on lipids is analyzed as a chemical profile, hence,the name MRM-profiling. We will also discuss the lipidomics capabilities, including LC-MS, available at the Metabolite Profiling Facility at Bindley Bioscience Center at Purdue University.

Light-sheet fluorescence microscopy (LSFM) enables large-scale, three-dimensional imaging at high imaging speeds with less phototoxicity and photobleaching. The Bruker MuVi microscope provides flexible illumination and detection configurations suitable for imaging samples from fields as diverse as cell and developmental biology, neuroscience, oncology, and plant research. In this presentation, you can expect to learn the advantages of light-sheet fluorescence microscopy and how this technique can be adapted to image a variety of live, fixed or cleared samples.

In this webinar we will discuss popular applications that utilize home-brew library preps with Illumina Sequencing as a downstream readout. This will include an overview of epigenetic methods designed to look at regions of open chromatin (ATAC-Seq), binding sites of DNA-associated proteins (ChIP-Seq/Cut and Run), and detection of long-range DNA interactions (Hi-C). Additionally, we will look at how Illumina Sequencing can be used as an effective strategy in genome wide CRISPR screens for quantification of sgRNAs as well as methods that allow the detection of transcriptional changes observed in the enriched or depletion knockout populations.

The Bruker 9.4T magnetic resonance (MR) scanner delivers in-vivo/ex-vivo images with high spatial and temporal resolution. Parallel with any MRI method on this machine, the compatible PET insert offers high resolution, high sensitivity, and high quantification accuracy, allowing for simultaneous PET/MR imaging in basic research and translational medicine. Applications in multiple fields are available with these advanced preclinical imaging solutions, including, but not limited to: oncology, neurology, cardiology, inflammation, functional and anatomical neuroimaging, orthopedics, cardiac imaging, and stroke models.